Week 3 HW: OPENTRONS
Paper: Accelerated high-throughput imaging and phenotyping system for small organisms
This paper details the creation of a high-throughput experimentation (HTE) platform built around duckweeds — specifically Lemna minor, a tiny aquatic plant with applications in bioremediation and biofuel research. To run large-scale evolutionary ecology experiments, the team combined an Opentrons OT-2 liquid handling robot with a custom autonomous imaging system, creating a pipeline capable of operating at a scale that would be practically impossible by hand. The central engineering challenge was that standard liquid handling robots are designed to work with, unsurprisingly, liquids. Duckweeds are solid floating plant fronds, which meant the OT-2 needed to be rethought for a very different kind of material. The researchers solved this by replacing the standard pipette tips on the OT-2’s P300 pipette heads with commercial inoculation loops. These loops exploit capillary action to gently lift individual fronds from the water’s surface, allowing the robot to pick and place solid biological matter with the same reliability it would otherwise bring to liquid transfers. This seemingly simple hardware modification had enormous practical consequences. By enabling automated handling of the plants, the team was able to design an experiment encompassing 6,000 individual microcosms spread across 2,000 distinct combinations of nutrients and microbes — a scale of experimental complexity that manual pipetting and plant placement could never realistically achieve, given how tedious and error-prone working with tiny floating organisms at high volume would be for human researchers.